{
  "_id": "6a1e11941d7bb097a0a5ec7c",
  "Package": "MeLSI",
  "Type": "Package",
  "Title": "Metric Learning for Statistical Inference in Microbiome Analysis",
  "Version": "1.1.1",
  "Authors@R": "c(person(\"Nathan\", \"Bresette\", email = \"nathanbresette04@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0003-1554-6006\")), person(\"Aaron C.\", \"Ericsson\", role = \"aut\", comment = c(ORCID = \"0000-0002-3053-7269\")), person(\"Carter\", \"Woods\", role = \"aut\", comment = c(ORCID = \"0009-0007-5345-2712\")), person(\"Ai-Ling\", \"Lin\", role = c(\"aut\", \"fnd\"), comment = c(ORCID = \"0000-0002-5197-2219\")))",
  "Description": "MeLSI (Metric Learning for Statistical Inference) is a\nnovel machine learning method for microbiome data analysis that\nlearns optimal distance metrics to improve statistical power in\ndetecting group differences. Unlike traditional distance\nmetrics (Bray-Curtis, Euclidean, Jaccard), MeLSI adapts to the\nspecific characteristics of your dataset to maximize separation\nbetween groups. The method uses an ensemble of weak learners to\nidentify which microbial features drive group differences,\nproviding both improved statistical power and biological\ninterpretability through feature importance weights.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/NathanBresette/MeLSI",
  "BugReports": "https://github.com/NathanBresette/MeLSI/issues",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, StatisticalMethod, Microbiome",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-06-01 20:01:39 UTC",
  "RemoteUrl": "https://github.com/bioc/MeLSI",
  "RemoteRef": "HEAD",
  "RemoteSha": "b8293765047fd6704996b800830618792d2efe08",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-01 23:05:55 UTC",
    "User": "root"
  },
  "Author": "Nathan Bresette [aut, cre] (ORCID:\n<https://orcid.org/0009-0003-1554-6006>),\nAaron C. Ericsson [aut] (ORCID:\n<https://orcid.org/0000-0002-3053-7269>),\nCarter Woods [aut] (ORCID: <https://orcid.org/0009-0007-5345-2712>),\nAi-Ling Lin [aut, fnd] (ORCID: <https://orcid.org/0000-0002-5197-2219>)",
  "Maintainer": "Nathan Bresette <nathanbresette04@gmail.com>",
  "MD5sum": "d8f4c0243a83fddee057ec98cb16a686",
  "_user": "bioc",
  "_type": "src",
  "_file": "MeLSI_1.1.1.tar.gz",
  "_fileid": "a273b700ee22cd8c0303780049e89737be30b1e13c8d273138df481f97ef2efe",
  "_filesize": 139247,
  "_sha256": "a273b700ee22cd8c0303780049e89737be30b1e13c8d273138df481f97ef2efe",
  "_created": "2026-06-01T23:05:55.000Z",
  "_published": "2026-06-01T23:11:16.271Z",
  "_jobs": [
    {
      "job": 78966481268,
      "time": 163,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7345155018"
    },
    {
      "job": 78966481314,
      "time": 282,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7345184220"
    },
    {
      "job": 78966481275,
      "time": 281,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7345183914"
    },
    {
      "job": 78966481266,
      "time": 118,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7345143452"
    },
    {
      "job": 78966481274,
      "time": 139,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7345149022"
    },
    {
      "job": 78965895872,
      "time": 272,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7345114706"
    },
    {
      "job": 78966481290,
      "time": 131,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7345146987"
    },
    {
      "job": 78966481298,
      "time": 155,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7345153093"
    },
    {
      "job": 78966481292,
      "time": 160,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7345154406"
    },
    {
      "job": 78966481288,
      "time": 160,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7345154192"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 3
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26787265693",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/MeLSI",
  "_commit": {
    "id": "b8293765047fd6704996b800830618792d2efe08",
    "author": "Nathan Bresette <nathanbresette04@gmail.com>",
    "committer": "Nathan Bresette <nathanbresette04@gmail.com>",
    "message": "Merge Bioconductor devel; bump to 1.1.1\n\nResolves version conflict from Bioconductor's automated release branch\nmanagement (1.1.0). Increment to 1.1.1 to carry forward the phyloseq\nImports→Suggests change on top of their devel baseline.\n\nCo-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>\n",
    "time": 1780344099
  },
  "_maintainer": {
    "name": "Nathan Bresette",
    "email": "nathanbresette04@gmail.com",
    "login": "nathanbresette",
    "description": "",
    "uuid": 148147840
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "vegan",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "BiocParallel",
      "role": "Suggests"
    },
    {
      "package": "Matrix",
      "role": "Suggests"
    },
    {
      "package": "microbiome",
      "role": "Suggests"
    },
    {
      "package": "phyloseq",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-40",
      "n": 27
    },
    {
      "week": "2025-41",
      "n": 3
    },
    {
      "week": "2025-42",
      "n": 13
    },
    {
      "week": "2025-45",
      "n": 1
    },
    {
      "week": "2025-48",
      "n": 20
    },
    {
      "week": "2025-49",
      "n": 13
    },
    {
      "week": "2025-52",
      "n": 11
    },
    {
      "week": "2026-04",
      "n": 2
    },
    {
      "week": "2026-05",
      "n": 1
    },
    {
      "week": "2026-09",
      "n": 7
    },
    {
      "week": "2026-16",
      "n": 2
    },
    {
      "week": "2026-23",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.1.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.0.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "statisticalmethod",
    "microbiome"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "nathanbresette",
      "count": 103,
      "uuid": 148147840
    },
    {
      "user": "jwokaty",
      "count": 2,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 250,
    "source": "https://www.bioconductor.org/packages/stats/bioc/MeLSI"
  },
  "_devurl": "https://github.com/nathanbresette/melsi",
  "_searchresults": 17,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/MeLSI.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/nathanbresette/melsi",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "clr_transform",
    "generate_test_data",
    "melsi",
    "plot_feature_importance",
    "plot_pcoa",
    "plot_vip"
  ],
  "_help": [
    {
      "page": "clr_transform",
      "title": "CLR Transformation for Microbiome Data",
      "topics": [
        "clr_transform"
      ]
    },
    {
      "page": "generate_test_data",
      "title": "Generate Synthetic Microbiome Data for Testing",
      "topics": [
        "generate_test_data"
      ]
    },
    {
      "page": "melsi",
      "title": "Run MeLSI Analysis",
      "topics": [
        "melsi"
      ]
    },
    {
      "page": "plot_feature_importance",
      "title": "Plot Feature Importance from MeLSI Analysis",
      "topics": [
        "plot_feature_importance"
      ]
    },
    {
      "page": "plot_pcoa",
      "title": "Plot PCoA from MeLSI Results",
      "topics": [
        "plot_pcoa"
      ]
    },
    {
      "page": "plot_vip",
      "title": "Plot VIP from MeLSI Results (User-Friendly Wrapper)",
      "topics": [
        "plot_vip"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/MeLSI/raw/HEAD/README.md",
  "_rundeps": [
    "cli",
    "cluster",
    "cpp11",
    "farver",
    "ggplot2",
    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "MASS",
    "Matrix",
    "mgcv",
    "nlme",
    "permute",
    "R6",
    "RColorBrewer",
    "rlang",
    "S7",
    "scales",
    "vctrs",
    "vegan",
    "viridisLite",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "melsi_tutorial.Rmd",
      "filename": "melsi_tutorial.html",
      "title": "MeLSI Tutorial: Basic Usage and Examples",
      "author": "Nathan Bresette",
      "engine": "knitr::rmarkdown",
      "headings": [
        "MeLSI Tutorial",
        "Abstract",
        "Introduction",
        "Comparison with Existing Bioconductor Packages",
        "Installation and Setup",
        "Basic Usage",
        "Step 1: Prepare Your Data",
        "Step 2: Data Preprocessing",
        "Step 3: Run MeLSI Analysis",
        "Comparison with Standard Methods",
        "Visualizing Results",
        "Variable Importance Plot (VIP)",
        "Principal Coordinates Analysis (PCoA)",
        "Advanced Usage: Custom Parameters",
        "Working with Bioconductor Packages",
        "Integration with phyloseq",
        "Summary",
        "Key Takeaways",
        "Next Steps",
        "Session Info"
      ],
      "created": "2025-10-02 14:53:34",
      "modified": "2026-02-23 19:38:41",
      "commits": 7
    }
  ],
  "_score": 5.008600171761918,
  "_indexed": true,
  "_nocasepkg": "melsi",
  "_universes": [
    "bioc",
    "nathanbresette"
  ],
  "_previous": "1.1.0",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.1",
      "date": "2026-06-01T23:10:02.000Z",
      "distro": "noble",
      "commit": "b8293765047fd6704996b800830618792d2efe08",
      "fileid": "24874902f8c19b275a08087134b466a86a159ae2845dc29ae07275f04e77f51b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26787265693"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.1",
      "date": "2026-06-01T23:09:48.000Z",
      "distro": "noble",
      "commit": "b8293765047fd6704996b800830618792d2efe08",
      "fileid": "11b226827a032583dc144b4dea3bb62a1812220bb29107b427a9cdd4195380a2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26787265693"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.1",
      "date": "2026-06-01T23:07:32.000Z",
      "commit": "b8293765047fd6704996b800830618792d2efe08",
      "fileid": "15f63c405c852d755b0c88b66b4a65713cf8575872e319fba7c82fe3dc423130",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26787265693"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.1",
      "date": "2026-06-01T23:07:46.000Z",
      "commit": "b8293765047fd6704996b800830618792d2efe08",
      "fileid": "3b9e60c50efd07cf007d696417072b25e8b0548e0ffcbbd150dea414e3a200a5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26787265693"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.1",
      "date": "2026-06-01T23:08:30.000Z",
      "commit": "b8293765047fd6704996b800830618792d2efe08",
      "fileid": "e5676b91ba6ee524e2dc7f688ef39d457f96915235480d13ab5bec197f1e8744",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26787265693"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.1",
      "date": "2026-06-01T23:07:36.000Z",
      "commit": "b8293765047fd6704996b800830618792d2efe08",
      "fileid": "1400391dac9372fb692f7b2dc452d7b3510f7c1f15951026f63e548c621bf811",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26787265693"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.1",
      "date": "2026-06-01T23:07:36.000Z",
      "commit": "b8293765047fd6704996b800830618792d2efe08",
      "fileid": "c720c2240e3677bb7fcd20047bd151b3ae5aaec1bb32bb776e28ba1934ade18d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26787265693"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.1",
      "date": "2026-06-01T23:07:39.000Z",
      "commit": "b8293765047fd6704996b800830618792d2efe08",
      "fileid": "c33110f1f916b8eaef52668dc00b677e0131839188950170a85d1ef0547843ba",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26787265693"
    }
  ]
}